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Gene expression and gene structure: an interview with Bert W. O'Malley.
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Molecular cloning of alcohol dehydrogenase genes of the yeast Pichia stipitis and identification of the fermentative ADH.
Two Pichia stipitis ADH genes (PsADH1 and PsADH2) were isolated by complementation of a Saccharomyces cerevisiae Adh(-)-mutant. The genes enabled the transformants to grow in the presence of antimycin A on glucose, to use ethanol as sole carbon source and made them sensitive to allylalcohol. The sequences of the genes showed similarities of 70-77% to sequences of ADH genes of Candida albicans, Kluyveromyces lactis, K. marxianus, and S. cerevisiae and about 60% homology to those of Schizosaccharomyces pombe and Aspergillus flavus. Southern hybridization experiments suggested that P. stipitis has only these two ADH genes. Both genes are located on the largest chromosome of P. stipitis. PsADH2 encodes for the ADH activity that is responsible for ethanol formation at oxygen limitation. The gene is regulated at the transcriptional level. Moreover, also in cells grown on ethanol, only PsADH2 transcript was found. PsADH1 transcript was detected under aerobic conditions on fermentable carbon sources.
Don't belittle Popper. Refutation cannot be refuted in biology, either.
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Seryl-tRNA synthetase is not responsible for the evolution of CUG codon reassignment in Candida albicans.
A number of Candida species translate the standard leucine-CUG codon as serine using a novel ser-tRNA(CAG). This tRNA, which has an unusual anticodon stem-loop structure, has been implicated in the evolution of this codon reassignment. However, such a sense codon reassignment might also require a change in the specificity of the cognate aminoacyl tRNA-synthetase, in this case the ser-tRNA synthetase. Here we describe the cloning and sequence analysis of the C. albicans seryl aminoacyl-tRNA synthetase (CaSerRS) gene (CaSES1). The predicted CaSerRS sequence shows a significant level of amino acid identity to SerRs from other organisms and fully complements a S. cerevisiae SerRS null strain without any apparent defect in growth rate. This suggests that the SerRS recognizes and charges S. cerevisiae ser-tRNAs with similar efficiency to that of the S. cerevisiae SerRS. Using an antibody raised against CaSerRS, we also demonstrate the presence of SerRS in a range of Candida spp. showing CUG codon reassignment. We conclude that the key element in CUG reassigment in Candida spp. is the tRNA that decodes the CUG codon rather than a SerRS structural change. The nucleotide sequence of the CaSES1 gene has been deposited at GenBank under Accession No. AF290915.
Modeling the interplay of generic and genetic mechanisms in cleavage, blastulation, and gastrulation.
Early development of multicellular organisms is marked by a rapid initial increase in their cell numbers, accompanied by spectacular morphogenetic processes leading to the gradual formation of organs of characteristic shapes. During morphogenesis, through differentiation under strict genetic control, cells become more and more specialized. Morphogenesis also requires coordinated cell movement and elaborate interactions between cells, governed by fundamental physical or generic principles. As a consequence, early development must rely on an intricate interplay of generic and genetic mechanisms. We present the results of computer simulations of the first nontrivial morphogenetic transformations in the life of multicellular organisms: initial cleavages, blastula formation, and gastrulation. The same model, which is based on the physical properties of individual cells and their interactions, describes all these processes. The genetic code determines the values of the model parameters. The model accurately reproduces the major steps of early development. It predicts that physical constraints strongly influence the timing of gastrulation. Gastrulation must occur prior to the appearance of dynamical instability, which would destabilize and eventually derail normal development. Within our model, to avoid the instability, we suddenly change the values of some of the model parameters. We interpret this change as a consequence of specific gene activity. After changing the physical characteristics of some cells, normal development resumes, and gastrulation proceeds.
New hypothesis on amino acid complementarity and its evaluation on TGF-beta(2)-related peptides.
A new hypothesis of amino acid complementarity based on the genetic code periodicity is presented and evaluated on the peptide pairs composed of the fragments of TGF-beta(2) protein (YIGKTPKI and YYIGKTPKIE) and corresponding complementary peptides [IYPLC(Acm)GLY, IIYTLWGLYL, IIYPLC(Acm)GLYL and IIYTLC(Acm)GLYL]. The ESI-MS and CD methods were used for monitoring of the complexation. It was found that heterodimeric structures are formed between the peptides and complementary peptides. No complexation appears in solutions of single components of the systems, nor in solutions containing the mixtures of TGF-beta(2) peptides or complementary peptides. CD measurements suggest that the conformation of peptides needed for complex formation is of the beta-structure type. The binding forces, which stabilize the complexes, consist mainly of hydrophobic interactions.
Novel regulatory interactions and activities of mammalian tRNA synthetases.
Aminoacyl-tRNA synthetases (ARSs) catalyze the attachment of specific amino acids to their cognate tRNAs, thereby ensuring the faithful translation of genetic code. In addition to their enzymatic function, these enzymes have been discovered to regulate various cellular functions such as tRNA export, ribosomal RNA synthesis, apoptosis, inflammation and angiogenesis in mammalian. The insights into the noncanonical activities of these enzymes have been obtained from their unique cellular localization, interacting partners, isoform generation and expression control. Mammalian ARSs also form a macromolecular protein complex with a few auxiliary factors. Although the physiological significance of this complex is poorly understood, it also supports the potential of mammalian ARSs as sophisticated multifunctional proteins for regulating various cellular procedures. In this review, the novel regulatory activities of mammalian ARSs will be discussed in different biological processes.
Genetic control of prion incubation period in mice.
The prion gene complex (Prn) is located on mouse chromosome 2 between the beta-2-microglobulin (B2m) and agouti (A) genes. Within this complex are the prion protein gene (Prn-p), which encodes the only identified macromolecule (PrP) that purifies with infectious scrapie agent, and a scrapie incubation time gene (Prn-i). Using a variety of restriction endonucleases, six allelic forms of the Prn-p gene have been distinguished by their patterns of restriction fragment length polymorphisms. We had previously shown that the exceptionally long scrapie incubation period of I/LnJ mice inoculated with the Chandler isolate (over 200 days) was due to the effects of a scrapie incubation time gene tightly linked to Prn-p. So far, this long scrapie incubation time allele has been found only in those inbred mouse strains (I/LnJ, P/J and IM) that have the b allele of Prn-p. It is not known whether the incubation time gene and prion protein gene are two distinct loci or are one and the same. Putative recombinants between the incubation time phenotype and Prn-p genotype have been observed, but this could be due to effects of other genes segregating in the population. Regardless of whether or not the incubation time and PrP genes are identical, if any differences were found in the amino acid sequences of PrP encoded by the different Prn-p alleles there would be important implications for interpretation of results on 'strains' of scrapie agent. It would not be necessary to invoke nucleic acid as the informational macromolecule of the scrapie agent because differences in prion 'strains' recovered from mice with different Prn-p genotypes need not be the result of host selection but could be due to differences in host-encoded PrP.
The role of the EST genes in yeast telomere replication.
We have recently completed a large mutant screen designed to identify new mutants of Saccharomyces cerevisiae with a telomerase-like defect. From this screen; 22 mutants were identified that mapped to three genes, called EST1, EST2 and EST3, as well as a novel EST-like mutation in a fourth gene, previously identified as CDC13. Mutations in each of these genes give rise to phenotypes that are indistinguishable from those observed when TLC1, encoding the yeast telomerase RNA, is deleted. In addition, genetic analysis indicates that all four genes function in the same pathway for telomere replication as defined by TLC1, the one known component of telomerase. This indicates that these genes encode factors that are essential in vivo for telomerase function. Genetic and biochemical analyses have shown that EST1 and CDC13 encode single-stranded telomeric DNA-binding proteins, suggesting that these two proteins may function to mediate access of telomerase to the end of the telomere.
The developmental field concept.
Identical anomalies produced by such different causes as aneuploidy, gene mutation, teratogenic chemicals, and certain surgical procedures show that embryonic primordia respond as units in the production of anomalies of anatomical structure. Hence, they must also act as units during normal ontogeny. The presence of identical malformations in different mammalian species identifies developmental and anatomical homology by virtue of descent from a common ancestor. These dys- and orthomorphogenetically reactive units are the equivalents of the classical experimental embryologist's epimorphic fields, which are those units of the embryo in which the development of complex structures appropriate to the species is determined and controlled in a spatially coordinated, temporally synchronous, and epimorphically hierarchical manner that expresses both species-nonspecific (that is, phylogenetic) and species-specific genetically coded developmental information. Thus, there is some merit in taking a long view of development.
Angular homeostasis. IX. Polygonal orbits with a moving target: implications for anomalous numbers of digits in congenital heart disease.
This paper explores properties of discrete processes in which a pursuer seeks a target that is moving at constant velocity r that is a fixed proportion of the speed of the pursuer. The pursuer is subjected to proportional angular homeostasis, so chosen that the number of steps per circuit is small. The orbits relative to the target may assume any of four forms: polygons that reverse their sense an infinite number of times; or polygons that after a finite number of reversals ultimately come to have an integer numbers of sides; or have a rational numbers of sides; or have an irrational number of sides that densely fill an annulus. None of the polygons is regular. In the parameter space, the boundary line between the first of these sets and the other three has a somewhat bizarre pattern and may possibly be fractal, but no proof is forthcoming. Unlike the pattern with a stationary target, there may be a set or catchment of diverse values of the speed ratio, r, and the correction coefficient, b that all result in figures of some specified number, n, of sides (although with vertices in differing locations). Catchments have been found for only those polygons that have the winding number of 1. The implications are discussed that this property has for the genetic coding of biological traits that are countable. Some attention is also paid to the relevance of polygons with few sides to ontogenic growth when the correction coefficient is cyclically arc- or time-dependent.
Translation of genetic information on the ribosome.
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Extrachromosomal DNA in bacteria.
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Intracellular protein degradation: from a vague idea, through the lysosome and the ubiquitin-proteasome system, and onto human diseases and drug targeting (Nobel lecture).
Between the 1950s and 1980s, scientists were focusing mostly on how the genetic code is transcribed to RNA and translated to proteins, but how proteins are degraded has remained a neglected research area. With the discovery of the lysosome by Christian de Duve it was assumed that cellular proteins are degraded within this organelle. Yet, several independent lines of experimental evidence strongly suggested that intracellular proteolysis is largely non-lysosomal, but the mechanisms involved remained obscure. The discovery of the ubiquitin-proteasome system resolved the enigma. We now recognize that degradation of intracellular proteins is involved in regulation of a broad array of cellular processes, such as the cell cycle and division, regulation of transcription factors, and assurance of the cellular quality control. Not surprisingly, aberrations in the system have been implicated in the pathogenesis of human disease, such as malignancies and neurodegenerative disorders, which led subsequently to an increasing effort to develop mechanism-based drugs.
Persistent biases in the amino acid composition of prokaryotic proteins.
Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins' amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism's biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the G + C content of the first codon position. An unexpected bias is driven, in many proteomes, by the AAN box of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction.
An extended Escherichia coli "selenocysteine insertion sequence" (SECIS) as a multifunctional RNA structure.
The genetic code, once thought to be rigid, has been found to permit several alternatives in its reading. Interesting alternative relates to the function of the UGA codon. Usually, it acts as a stop codon, but it can also direct the incorporation of the amino acid selenocysteine into a polypeptide. UGA-directed selenocysteine incorporation requires a cis-acting mRNA element called the "selenocysteine insertion sequence" (SECIS) that can form a stem-loop RNA structure. Here we discuss our investigation on the E. coli SECIS. This includes the follows: 1) The nature of the minimal E. coli SECIS. We found that in E. coli only the upper-stem and loop of 17 nucleotides of the SECIS is necessary for selenocysteine incorporation on the condition that it is located in the proper distance from the UGA [34]; 2) The upper stem and loop structure carries a bulged U residue that is required for selenocysteine incorporation [34] because of its interaction with SelB; and 3) We described an extended fdhF SECIS that includes the information for an additional function: The prevention of UGA readthrough under conditions of selenium deficiency [35]. This information is contained in a short mRNA region consisting of a single C residue adjacent to the UGA on its downstream side, and an additional segment consisting of the six nucleotides immediately upstream from it. These two regions act independently and additively and probably through different mechanisms. The single C residue acts as itself; the upstream region acts at the level of the two amino acids, arginine and valine, for which it codes. These two codons at the 5' side of the UGA correspond to the ribosomal E and P sites. Finally, we present a model for the E. coli fdhF SECIS as a multifunctional RNA structure containing three functional elements. Depending on the availability of selenium the SECIS enables one of two alternatives for the translational machinery: Either selenocysteine incorporation into a polypeptide or termination of the polypeptide chain.
Ribosomal crystallography: peptide bond formation and its inhibition.
Ribosomes, the universal cellular organelles catalyzing the translation of genetic code into proteins, are protein/RNA assemblies, of a molecular weight 2.5 mega Daltons or higher. They are built of two subunits that associate for performing protein biosynthesis. The large subunit creates the peptide bond and provides the path for emerging proteins. The small has key roles in initiating the process and controlling its fidelity. Crystallographic studies on complexes of the small and the large eubacterial ribosomal subunits with substrate analogs, antibiotics, and inhibitors confirmed that the ribosomal RNA governs most of its activities, and indicated that the main catalytic contribution of the ribosome is the precise positioning and alignment of its substrates, the tRNA molecules. A symmetry-related region of a significant size, containing about two hundred nucleotides, was revealed in all known structures of the large ribosomal subunit, despite the asymmetric nature of the ribosome. The symmetry rotation axis, identified in the middle of the peptide-bond formation site, coincides with the bond connecting the tRNA double-helical features with its single-stranded 3' end, which is the moiety carrying the amino acids. This thus implies sovereign movements of tRNA features and suggests that tRNA translocation involves a rotatory motion within the ribosomal active site. This motion is guided and anchored by ribosomal nucleotides belonging to the active site walls, and results in geometry suitable for peptide-bond formation with no significant rearrangements. The sole geometrical requirement for this proposed mechanism is that the initial P-site tRNA adopts the flipped orientation. The rotatory motion is the major component of unified machinery for peptide-bond formation, translocation, and nascent protein progression, since its spiral nature ensures the entrance of the nascent peptide into the ribosomal exit tunnel. This tunnel, assumed to be a passive path for the growing chains, was found to be involved dynamically in gating and discrimination.